Bottom Line:
During assembly, HLA class II molecules associate with the invariant chain.By mass spectrometry, we have now characterized peptides that are naturally present in HLA-DQ2.This analysis revealed that 22 variants of Ii-derived peptides are associated with HLA-DQ2.

ABSTRACTDuring assembly, HLA class II molecules associate with the invariant chain. As the result, the peptide-binding groove is occupied by an invariant chain peptide termed CLIP (class-II-associated invariant chain peptide; sequence MRMATPLLM). By mass spectrometry, we have now characterized peptides that are naturally present in HLA-DQ2. This analysis revealed that 22 variants of Ii-derived peptides are associated with HLA-DQ2. Strikingly, the large majority of those do not contain the conventional CLIP sequence MRMATPLLM, but instead a peptide that partially overlaps with CLIP, sequence TPLLMQALPM. Peptide binding studies indicate that this alternative CLIP peptide has superior HLA-DQ2 binding properties compared to the conventional CLIP and that the minimal nine-amino-acid binding core consists of the sequence PLLMQALPM, findings that could be corroborated by molecular simulation. The alternative CLIP peptide was also found to be present in HLA-DQ2 molecules isolated from human thymus. Moreover, the alternative CLIP peptide was also found in association with HLA-DQ8. Together, these results indicate that HLA-DQ2 and HLA-DQ8 associate with an alternative CLIP sequence, a property that may relate to the strong association between HLA-DQ molecules and human autoimmune diseases.

Fig3: Computer modeling of DQ2-CLIP in association with HLA-DQ2 based on the known DQ2-structure. A Side view of the DQ2-CLIP peptide (Ii 94–104) as it appears in complex with HLA-DQ2. B Shown is the TCR view of HLA-DQ2 (A1*0501/B1*0201) in complex with the DQ2-CLIP peptide (94–104 of Ii; core nonamer 96–104). The HLA-DQ2 molecule is shown in a van der Waals surface representation color coded according to the atomic charges (positive, blue; negative, red; neutral, gray); the surfaces for four residues (α76Arg, β61Trp, β70Arg, β71Lys) are transparent so that the respective residues can all be made visible. The peptide is shown in space filling mode (atomic color code: carbon, green; oxygen, red; nitrogen, blue; hydrogen, white; sulfur, yellow)

Mentions:
Additionally, modeling of HLA-DQ2 complexed with the peptide PLLMQALPM showed that it fits well in the groove of HLA-DQ2 (Fig. 3a and b). Moreover, it is predicted to bind better than the conventional CLIP peptide MRMATPLLM (unpublished data), a prediction that is confirmed by the observed superior binding of DQ2-CLIP (Fig. 2a).Fig. 3

Fig3: Computer modeling of DQ2-CLIP in association with HLA-DQ2 based on the known DQ2-structure. A Side view of the DQ2-CLIP peptide (Ii 94–104) as it appears in complex with HLA-DQ2. B Shown is the TCR view of HLA-DQ2 (A1*0501/B1*0201) in complex with the DQ2-CLIP peptide (94–104 of Ii; core nonamer 96–104). The HLA-DQ2 molecule is shown in a van der Waals surface representation color coded according to the atomic charges (positive, blue; negative, red; neutral, gray); the surfaces for four residues (α76Arg, β61Trp, β70Arg, β71Lys) are transparent so that the respective residues can all be made visible. The peptide is shown in space filling mode (atomic color code: carbon, green; oxygen, red; nitrogen, blue; hydrogen, white; sulfur, yellow)

Mentions:
Additionally, modeling of HLA-DQ2 complexed with the peptide PLLMQALPM showed that it fits well in the groove of HLA-DQ2 (Fig. 3a and b). Moreover, it is predicted to bind better than the conventional CLIP peptide MRMATPLLM (unpublished data), a prediction that is confirmed by the observed superior binding of DQ2-CLIP (Fig. 2a).Fig. 3

Bottom Line:
During assembly, HLA class II molecules associate with the invariant chain.By mass spectrometry, we have now characterized peptides that are naturally present in HLA-DQ2.This analysis revealed that 22 variants of Ii-derived peptides are associated with HLA-DQ2.

ABSTRACTDuring assembly, HLA class II molecules associate with the invariant chain. As the result, the peptide-binding groove is occupied by an invariant chain peptide termed CLIP (class-II-associated invariant chain peptide; sequence MRMATPLLM). By mass spectrometry, we have now characterized peptides that are naturally present in HLA-DQ2. This analysis revealed that 22 variants of Ii-derived peptides are associated with HLA-DQ2. Strikingly, the large majority of those do not contain the conventional CLIP sequence MRMATPLLM, but instead a peptide that partially overlaps with CLIP, sequence TPLLMQALPM. Peptide binding studies indicate that this alternative CLIP peptide has superior HLA-DQ2 binding properties compared to the conventional CLIP and that the minimal nine-amino-acid binding core consists of the sequence PLLMQALPM, findings that could be corroborated by molecular simulation. The alternative CLIP peptide was also found to be present in HLA-DQ2 molecules isolated from human thymus. Moreover, the alternative CLIP peptide was also found in association with HLA-DQ8. Together, these results indicate that HLA-DQ2 and HLA-DQ8 associate with an alternative CLIP sequence, a property that may relate to the strong association between HLA-DQ molecules and human autoimmune diseases.